After the early period when your explorers discover pirate bases in the course of their exploration, it does get trickier to find pirate bases. This is the part of the game where long range scanners finally pay their due, IMO. I install them on all my spaceports - the range is very big, especially with upgrades, and you can see any pirates trying to build cheeky bases nearby and monitor their ships in the area - and build a series of ships designed to suss out pirate stuff. I use the escort class, mainly because I don't use it for anything else, and I like using them as combat recon to take out small mining stations their find themselves. Fit the long range scanner, a lot of extra fuel cells to power the scanner and if you're like me, some weapons and a few shields. Then just queue up orders for it to fly to systems where it's possible a pirate base is hiding, or if you want to be more safe, queue up travel points in deep space nearby a few suspect systems. If the recon finds a pirate base, then it'll appear on the map as a flag like always. If it finds a mining station, you won't get a warning, but if you're paying attention you can divert it or some other ships to destroy it.
Also, stealing their territory map only works if they've built a Criminal Network and therefore actually have territory. You'll need to snatch their operations map instead, as suggested above. Their bases will remain on the map as flags after the operations map wears off - it only lasts a minute or so - but you should pause to take note of other places the pirates are operating in. You may well find another empire, independent colony, etc.
< Message edited by Starke -- 7/16/2013 7:29:25 PM >